assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCF_009664535.1_ASM966453v1	NZ_CP045941	Shigella flexneri 2a strain AUSMDU00010535 chromosome, complete genome	1	720247-720348	1	CRISPRCasFinder	no		csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	Orphan	TTGTTGATGTTGTTGTGTTTTGTA	24	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	NA,NA|55aa|down_0|NZ_CP045941.1_720388_720553_-	NA|115aa|up_9|NZ_CP045941.1_707918_708263_-	PRK11424, PRK11424, DNA-binding transcriptional activator TdcR; Provisional	NA|313aa|up_8|NZ_CP045941.1_708452_709391_+	PRK10341, PRK10341, transcriptional regulator TdcA	NA|330aa|up_7|NZ_CP045941.1_709489_710479_+	PRK08638, PRK08638, bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB	NA|444aa|up_6|NZ_CP045941.1_710500_711832_+	PRK13629, PRK13629, threonine/serine transporter TdcC; Provisional	NA|403aa|up_5|NZ_CP045941.1_711857_713066_+	PRK12379, PRK12379, propionate kinase	NA|765aa|up_4|NZ_CP045941.1_713099_715394_+	cd01678, PFL1, Pyruvate formate lyase 1	NA|130aa|up_3|NZ_CP045941.1_715407_715797_+	PRK11401, PRK11401, enamine/imine deaminase	NA|455aa|up_2|NZ_CP045941.1_715868_717233_+	PRK15040, PRK15040, L-serine ammonia-lyase	NA|444aa|up_1|NZ_CP045941.1_717507_718839_+	TIGR00814, membrane_transport_protein_YhjV, serine transporter	NA|437aa|up_0|NZ_CP045941.1_718866_720177_+	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|55aa|down_0|NZ_CP045941.1_720388_720553_-	NA	NA|234aa|down_1|NZ_CP045941.1_720575_721277_-	COG1741, COG1741, Pirin-related protein [General function prediction only]	NA|299aa|down_2|NZ_CP045941.1_721381_722278_+	cd08431, PBP2_HupR, The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold	NA|123aa|down_3|NZ_CP045941.1_722484_722853_-	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|329aa|down_4|NZ_CP045941.1_723145_724132_-	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]	NA|129aa|down_5|NZ_CP045941.1_724201_724588_-	COG2259, COG2259, Predicted membrane protein [Function unknown]	NA|100aa|down_6|NZ_CP045941.1_724683_724983_-	pfam13997, YqjK, YqjK-like protein	NA|135aa|down_7|NZ_CP045941.1_724972_725377_-	COG5393, COG5393, Predicted membrane protein [Function unknown]	NA|102aa|down_8|NZ_CP045941.1_725379_725685_-	COG4575, ElaB, Uncharacterized conserved protein [Function unknown]	NA|128aa|down_9|NZ_CP045941.1_726223_726607_-	PRK10629, PRK10629, EnvZ/OmpR regulon moderator MzrA
GCF_009664535.1_ASM966453v1	NZ_CP045941	Shigella flexneri 2a strain AUSMDU00010535 chromosome, complete genome	2	1140502-1140636	2	CRISPRCasFinder	no		csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	Orphan	ATCTGATGATATTTTTCCCTGAAGGCTGCCGGGGAGATATT	41	1	1	1140543-1140595	NZ_CP045941.1_2510955-2511007	NA	1	1	Orphan	csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	NA,NA|65aa|down_3|NZ_CP045941.1_1148513_1148708_+	NA|350aa|up_9|NZ_CP045941.1_1130042_1131092_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|up_8|NZ_CP045941.1_1131072_1131834_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional	NA|209aa|up_7|NZ_CP045941.1_1131827_1132454_+	PRK00312, pcm, protein-L-isoaspartate(D-aspartate) O-methyltransferase	NA|380aa|up_6|NZ_CP045941.1_1132593_1133733_+	PRK10871, nlpD, murein hydrolase activator NlpD	NA|331aa|up_5|NZ_CP045941.1_1133795_1134788_+	PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated	NA|136aa|up_4|NZ_CP045941.1_1134907_1135315_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|198aa|up_3|NZ_CP045941.1_1135461_1136055_+	COG0163, UbiX family flavin prenyltransferase [Coenzyme transport and metabolism]	NA|188aa|up_2|NZ_CP045941.1_1137274_1137838_-	pfam07022, Phage_CI_repr, Bacteriophage CI repressor helix-turn-helix domain	NA|84aa|up_1|NZ_CP045941.1_1138002_1138254_+	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|699aa|up_0|NZ_CP045941.1_1138255_1140352_+	pfam09299, Mu-transpos_C, Mu transposase, C-terminal	NA|371aa|down_0|NZ_CP045941.1_1141803_1142915_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|256aa|down_1|NZ_CP045941.1_1144300_1145068_+	COG1349, GlpR, Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]	NA|854aa|down_2|NZ_CP045941.1_1145876_1148438_-	PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional	NA|65aa|down_3|NZ_CP045941.1_1148513_1148708_+	NA	NA|118aa|down_4|NZ_CP045941.1_1149501_1149855_+	pfam11756, YgbA_NO, Nitrous oxide-stimulated promoter	NA|693aa|down_5|NZ_CP045941.1_1149891_1151970_-	PRK15429, PRK15429, formate hydrogenlyase transcriptional activator FlhA	NA|337aa|down_6|NZ_CP045941.1_1152043_1153054_-	TIGR02124, Hydrogenase_expression/formation_protein_HypE, hydrogenase expression/formation protein HypE	NA|374aa|down_7|NZ_CP045941.1_1153050_1154172_-	PRK15062, PRK15062, hydrogenase isoenzymes formation protein HypD; Provisional	NA|91aa|down_8|NZ_CP045941.1_1154171_1154444_-	PRK10409, PRK10409, HypC/HybG/HupF family hydrogenase formation chaperone	NA|291aa|down_9|NZ_CP045941.1_1154434_1155307_-	PRK10463, PRK10463, hydrogenase nickel incorporation protein HypB; Provisional
GCF_009664535.1_ASM966453v1	NZ_CP045941	Shigella flexneri 2a strain AUSMDU00010535 chromosome, complete genome	3	1611800-1611917	3	CRISPRCasFinder	no		csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	Orphan	CCGAGCCGTAGGCCGGATAAGGCGTTCACGC	31	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	NA,NA	NA|157aa|up_9|NZ_CP045941.1_1600721_1601192_+	PRK10128, PRK10128, 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional	NA|317aa|up_8|NZ_CP045941.1_1601232_1602183_-	PRK09956, PRK09956, ISNCY family transposase	NA|397aa|up_7|NZ_CP045941.1_1602375_1603566_-	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|420aa|up_6|NZ_CP045941.1_1603562_1604822_-	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|543aa|up_5|NZ_CP045941.1_1604811_1606440_-	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|453aa|up_4|NZ_CP045941.1_1606712_1608071_+	PRK11273, glpT, glycerol-3-phosphate transporter	NA|359aa|up_3|NZ_CP045941.1_1608075_1609152_+	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|217aa|up_2|NZ_CP045941.1_1609614_1610265_+	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|85aa|up_1|NZ_CP045941.1_1610318_1610573_-	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|377aa|up_0|NZ_CP045941.1_1610572_1611703_-	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|762aa|down_0|NZ_CP045941.1_1611936_1614222_-	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|425aa|down_1|NZ_CP045941.1_1615092_1616366_-	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|552aa|down_2|NZ_CP045941.1_1616384_1618040_+	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|645aa|down_3|NZ_CP045941.1_1618049_1619984_+	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|241aa|down_4|NZ_CP045941.1_1620111_1620834_-	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|876aa|down_5|NZ_CP045941.1_1620980_1623608_+	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|208aa|down_6|NZ_CP045941.1_1625441_1626065_+	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|390aa|down_7|NZ_CP045941.1_1628413_1629582_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|53aa|down_8|NZ_CP045941.1_1631134_1631293_+	COG2373, COG2373, Large extracellular alpha-helical protein [General function prediction only]	NA|550aa|down_9|NZ_CP045941.1_1631856_1633506_+	COG5445, COG5445, Predicted secreted protein [Function unknown]
GCF_009664535.1_ASM966453v1	NZ_CP045941	Shigella flexneri 2a strain AUSMDU00010535 chromosome, complete genome	4	2249297-2249420	4	CRISPRCasFinder	no	c2c9_V-U4,DEDDh	csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	Unclear	CGACCCCCACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA	43	0	0	NA	NA	NA	1	1	Unclear	csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	NA,NA|75aa|down_7|NZ_CP045941.1_2258005_2258230_-,NA|30aa|down_8|NZ_CP045941.1_2258316_2258406_+	NA|335aa|up_9|NZ_CP045941.1_2236543_2237548_+	PRK10190, PRK10190, L,D-transpeptidase; Provisional	NA|79aa|up_8|NZ_CP045941.1_2237610_2237847_-	PRK15396, PRK15396, major outer membrane lipoprotein	NA|471aa|up_7|NZ_CP045941.1_2238157_2239570_-	PRK09206, PRK09206, pyruvate kinase PykF	NA|70aa|up_6|NZ_CP045941.1_2240902_2241112_+	PRK10292, PRK10292, fumarate hydratase FumD	NA|209aa|up_5|NZ_CP045941.1_2241567_2242194_+	PRK09898, PRK09898, ferredoxin-like protein	NA|213aa|up_4|NZ_CP045941.1_2244328_2244967_+	PRK09947, PRK09947, YdhW family putative oxidoreductase system protein	NA|223aa|up_3|NZ_CP045941.1_2245030_2245699_+	TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein	NA|262aa|up_2|NZ_CP045941.1_2245695_2246481_+	PRK15006, PRK15006, thiosulfate reductase cytochrome B subunit; Provisional	NA|271aa|up_1|NZ_CP045941.1_2246484_2247297_+	PRK09946, PRK09946, hypothetical protein; Provisional	NA|102aa|up_0|NZ_CP045941.1_2248856_2249162_-	PRK11118, PRK11118, putative monooxygenase; Provisional	NA|419aa|down_0|NZ_CP045941.1_2249734_2250991_+	PRK09945, PRK09945, hypothetical protein; Provisional	NA|458aa|down_1|NZ_CP045941.1_2251031_2252405_-	PRK01766, PRK01766, multidrug efflux protein; Reviewed	NA|214aa|down_2|NZ_CP045941.1_2252619_2253261_+	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional	NA|383aa|down_3|NZ_CP045941.1_2253300_2254449_-	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase	NA|404aa|down_4|NZ_CP045941.1_2254739_2255951_-	PRK11043, PRK11043, Bcr/CflA family multidrug efflux MFS transporter	NA|311aa|down_5|NZ_CP045941.1_2256063_2256996_+	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional	NA|342aa|down_6|NZ_CP045941.1_2256992_2258018_-	PRK10703, PRK10703, HTH-type transcriptional repressor PurR	NA|75aa|down_7|NZ_CP045941.1_2258005_2258230_-	NA	NA|30aa|down_8|NZ_CP045941.1_2258316_2258406_+	NA	NA|390aa|down_9|NZ_CP045941.1_2258571_2259741_+	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]
GCF_009664535.1_ASM966453v1	NZ_CP045941	Shigella flexneri 2a strain AUSMDU00010535 chromosome, complete genome	5	3196537-3196685	5,1	CRISPRCasFinder,PILER-CR	no		csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	Orphan	ATTTCTAAGCTGCCTGTACGGCAGTGAAC,ATTTCTAAGCTGCCTGTACGGCAGTGAAC	29,29	0	0	NA	NA	I-F:I-F	2,2	2	Orphan	csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	NA,NA	NA|431aa|up_9|NZ_CP045941.1_3181623_3182916_-	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional	NA|448aa|up_8|NZ_CP045941.1_3183006_3184350_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|204aa|up_7|NZ_CP045941.1_3184360_3184972_-	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|1343aa|up_6|NZ_CP045941.1_3185126_3189155_-	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|165aa|up_5|NZ_CP045941.1_3189289_3189784_-	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|322aa|up_4|NZ_CP045941.1_3190327_3191293_+	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|589aa|up_3|NZ_CP045941.1_3191415_3193182_+	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|574aa|up_2|NZ_CP045941.1_3193182_3194904_+	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|235aa|up_1|NZ_CP045941.1_3194945_3195650_+	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|73aa|up_0|NZ_CP045941.1_3195934_3196153_+	PRK00276, infA, translation initiation factor IF-1; Validated	NA|759aa|down_0|NZ_CP045941.1_3196896_3199173_-	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|107aa|down_1|NZ_CP045941.1_3199203_3199524_-	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|75aa|down_2|NZ_CP045941.1_3199846_3200071_+	PRK09937, PRK09937, cold shock-like protein CspD	NA|649aa|down_3|NZ_CP045941.1_3200143_3202090_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|372aa|down_4|NZ_CP045941.1_3202086_3203202_-	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|319aa|down_5|NZ_CP045941.1_3203352_3204309_+	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|553aa|down_6|NZ_CP045941.1_3204305_3205964_-	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|232aa|down_7|NZ_CP045941.1_3207130_3207826_+	PRK05420, PRK05420, aquaporin Z; Provisional	NA|410aa|down_8|NZ_CP045941.1_3208266_3209495_+	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|300aa|down_9|NZ_CP045941.1_3209618_3210518_+	COG2431, COG2431, Predicted membrane protein [Function unknown]
GCF_009664535.1_ASM966453v1	NZ_CP045941	Shigella flexneri 2a strain AUSMDU00010535 chromosome, complete genome	6	4014386-4014501	6	CRISPRCasFinder	no		csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	Orphan	AACGCCTGATGCGACGCTGACGCGTCTTATC	31	0	0	NA	NA	NA	1	1	Orphan	csa3,RT,cas3,DEDDh,c2c9_V-U4,DinG,PrimPol	NA,NA	NA|393aa|up_9|NZ_CP045941.1_4002401_4003580_-	TIGR00899, Sugar_efflux_transporter_A, sugar efflux transporter	NA|44aa|up_8|NZ_CP045941.1_4003681_4003813_-	pfam15894, SgrT, Inhibitor of glucose uptake transporter SgrT	NA|552aa|up_7|NZ_CP045941.1_4003901_4005557_+	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|328aa|up_6|NZ_CP045941.1_4005720_4006704_+	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|537aa|up_5|NZ_CP045941.1_4006679_4008290_+	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|233aa|up_4|NZ_CP045941.1_4008273_4008972_+	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|255aa|up_3|NZ_CP045941.1_4009085_4009850_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|293aa|up_2|NZ_CP045941.1_4009935_4010814_-	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|567aa|up_1|NZ_CP045941.1_4011152_4012853_+	PRK04123, PRK04123, ribulokinase; Provisional	NA|501aa|up_0|NZ_CP045941.1_4012863_4014366_+	PRK02929, PRK02929, L-arabinose isomerase; Provisional	NA|232aa|down_0|NZ_CP045941.1_4014565_4015261_+	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|784aa|down_1|NZ_CP045941.1_4015335_4017687_+	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|969aa|down_2|NZ_CP045941.1_4017851_4020758_+	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|220aa|down_3|NZ_CP045941.1_4020769_4021429_+	PRK10158, PRK10158, bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA|272aa|down_4|NZ_CP045941.1_4021545_4022361_-	PRK09430, djlA, co-chaperone DjlA	NA|785aa|down_5|NZ_CP045941.1_4022615_4024970_+	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|429aa|down_6|NZ_CP045941.1_4025022_4026309_+	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|330aa|down_7|NZ_CP045941.1_4026308_4027298_+	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|274aa|down_8|NZ_CP045941.1_4027294_4028116_+	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|126aa|down_9|NZ_CP045941.1_4028118_4028496_+	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed
